The aim of immunohistochemistry and immunocytochemistry is to reveal specific antigens in cells and tissue samples. Those techniques are based on an antigen-antibody reaction and visualization of its product in microscopic examination. The precursor of this new diagnostic procedure was an immunofluorescent reaction in frozen tissue samples performed by Albert Coons in 1940. Then the immunohistochemical techniques were perfected to increase sensitivity and specificity. Currently it is hard to imagine a modern pathological examination without immunohistochemistry. At the end of XXth century it was believed that 75% of cases is possible to be diagnosed due to immunohistochemical stains. Microscopic examination of endocrine glands tissue samples is extremely difficult because of coexistence of the presence of neoplasms and endocrine dysfunction. It is necessary to establish the type of hormones in the cells of the endocrine system lesions to make a proper diagnosis. Thanks to the use of antibodies against hormones and its precursors it becomes possible. At present most of the antigens are easily detected in both: formalin fixed paraffin embedded tissues samples and ethanol fixed cytological smears so immunohistochemocal and immunocytological stains can be a part of routine diagnostic procedures in pathology. However most of the biologically active substances are revealed in many organs and tissues and it is necessary to perform a satisfactory immunohistochemical panel to be sure the diagnosis. It is important to notice that there is no need to make a wide panel of antibodies in all of the cases and the economical aspect of examination is also important. Of course immunohistochemistry sometimes is the guarantee of proper diagnosis but in some cases too wide panel of antibodies can be a loss for the patient and for medical department. We discussed the proper diagnostic procedures and immunohistochemical profile in pathological lesions of endocrine system (thyroid and adrenal gland, adenohypophysis, neuroendocrine tumours and some hormones-secreting tumours of gonads).